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openBIS master data are:

  1. Spaces
  2. Experiment/Collection types
  3. Object types
  4. Dataset types
  5. Property types


How to register a Space 


  1. Go to Admin → Spaces

     
  2. Go to Add Space at the bottom of the page



  3. Enter a Code and, if you wish, a Description for the Space



  4. Save


How to Register an Experiment/Collection type


  1. Go to Admin → Types → CollectionTypes

  2. Select Add at the bottom of the page



  3. Now enter the Code for the Experiment/Collection type. E.g. for a microscopy experiment, the code could be EXPERIMENT_MICROSCOPY.

  4. Description: fill in this field if you want to provide some details about this Collection/Experiment type
  5. Validation plugin: If you want to have data validation, a script needs to be written (=validation plugin) and can be selected from here. An example of data validation would be if you have two properties, one called Start date and one called End date, the End date should never be earlier than the Start date.

  6. Add properties. These are the fields that you need for this Collection/Experiment. Select Entity: Add at the bottom of the page. You have two options:

    1. choose from a list of existing properties

      The dropdown Property type (see screenshot above) gives you the list of all registered properties in openBIS. The full list of registered properties is under Admin → Types → Browse Property Types

    2. create a new property


      To register a new property you need to provide:

      1. Code: this is the unique identifier for this property. Codes only take alphanumeric characters and no spaces.
      2. Label: This is what is shown in the user interface. Labels are not unique.
      3. Description: this field provides a hint to what should be entered in the property field
      4. Data type: what type of property this is (see below for list of available Data Types)
      5. Handled by plugin: if this is a dynamic property or managed property, whose value is computed by a plugin, this needs to be specified here
      6. Mandatory: It is possible to set mandatory properties 

      After choosing the data type, two new fields are added to the widget in the screenshot above:



      1. Section: sections are ways of grouping together some properties. For example properties such as Storage ConditionStorage locationBox Name, can all belong to a Section called Storage information. There are no pre-defined Sections in the system, they always need to be defined by an admin by entering the desired Section Name in the Section field.
      2. Position after: this allows to specify the position of the Property in the user interface.

Data Types available in openBIS

The following data types are available in openBIS:



  1. Boolean: True or false
  2. Controlled Vocabulary: list of values to choose form. Only 1 value can be selected from a list
  3. Hyperlink: URL
  4. Integer: integer number
  5. Material: not to be used, it will be soon discontinued
  6. Multiline varchar: long text
  7. Real: decimal number 
  8. Timestamp: date (and timestamp)
  9. Varchar: one-line text
  10. XML: to be used for Managed properties and for spreadsheet fields 


Controlled Vocabularies

A Controlled Vocabulary is a pre-defined list of terms to choose from. Only one term can be selected.

When you choose CONTROLLEDVOCABULARY as data type, you can then either choose from existing vocabularies (drop down) or create a new vocabulary (+ next to dropdown).

To create a new vocabulary, you need to enter the Code and the list of terms belonging to the vocabulary. 

For example, we want to have a drop down list for different storage conditions: -80°C, -20°C, 4°C, room temperature.

We can use STORAGE_CONDITION as vocabulary code (this is the unique identifier of this vocabulary). Then we can specify the list of terms, either in the interface or we can load them from a file.

Vocabulary terms have codes and labels. The code is always the unique identifier and should be written with alphanumeric characters and no spaces; labels are shown in the user interface (if present) and they can be written as normal text.

Taking as example the Storage conditions mentioned above, we could have the following codes and labels:

             

CodeLabel
MINUS_80-80°C
MINUS_20-20°C
4+4°C
RTroom temperature

 

  1. specify list of terms in the interface. 


In this case, in the Terms field, we can only enter vocabulary codes (not labels) separated by a comma, or alternatively 1 code per line. If we use this approach, we need to add the label in a second step, by editing the Controlled Vocabulary.

2. load terms from a file


In this case a tab separated file that contains at least one column for code and one column for label can be uploaded. Following this procedure, codes and labels can be added in one single step.


Editing Controlled Vocabularies

It is possible to edit existing vocabulary terms, for example to add a label, and also to add new terms to an existing vocabulary.

  1. Go to Admin→ Vocabularies

 

2. Select the desired vocabulary in the table (click on the blue link)

3. Add a new term by selecting Entity: Add at the bottom of the page

or

Edit an existing term by selecting it in the table and then going to Entity:Edit at the bottom of the page.

 


How to Register an Object type


  1. Go to Admin → Types → Object Types

  2. To register a new type select Entity:Add at the bottom of the page. To edit an existing Object type, select the desired type from the table and go to Entity:Edit at the bottom of the page.



  3. In the Object Type registration page a few fields need to be filled in (see screenshot below)
    1. Code: the name of the object type. Codes can only have alpha-numeric characters.
    2. Description: fill in this field if you want to provide some details about this Object type.
    3. Validation plugin: If you want to have data validation, a script needs to be written (=validation plugin) and can be selected from here. An example of data validation would be if you have two properties, one called Start date and one called End date, the End date should never be earlier than the Start date.
    4. Listable: if checked, the object appears in the "Browse object" dropdown of the admin UI. Please note that this does not apply to the ELN UI.
    5. Show container: if checked, container objects are shown. Please note that this does not apply to the ELN UI.
    6. Show parents: if checked, parents of the object are shown 
    7. Unique subcodes: this applies to contained samples, which can have unique subcodes if this property is checked. Please note that the concept of container and contained samples are not used in the ELN.
    8. Generate Codes automatically: check this if you want to have Object codes automatically generated by openBIS
    9. Show parent metadata: check this if you wnat to have parents metadata shown. If not, only parents' codes will be shown
    10. Generated Code prefix: this is the prefix of the code used for each new registered object. A good convention is to use the first 3 letters of the Object Type Code ad Code Prefix. E.g. If the Object Type Code is CHEMICAL, the Code prefix can be CHE. Each new chemical registered in openBIS will have CHE1, CHE2, CHE3... CHEn as codes.

  4. Add properties: these are the fields that you need for this Object Type. Select Entity: Add at the bottom of the page. See HowtoRegisteranExperiment/Collectiontype.


How to register a Data Set type


  1. Go to Admin → Types → Data Set Types

  2. Select Entity:Add at the bottom of the page
  3. The Data Set Type registration form has the following fields:
    1. Code: name of the data set (e.g. RAW_DATA). Code can only take alphanumeric characters and cannot contain spaces.
    2. Description: you can provide a short description of the data set
    3. Validation plugin:
    4. Disallow deletion: if checked, all datasets belonging to this type cannot be deleted
    5. Main Data Set Pattern: if there is just one data set matching the chosen 'main data set' pattern, it will be automatically displayed. A regular expression is expected. E.g.: '.*.jpg'
    6. Main Data Set Path: The path (relative to the top directory of a data set) that will be used as a starting point of 'main data set' lookup. E.g. 'original/images/'
  4. Add properties: these are the fields that you need for this Object Type. Select Entity: Add at the bottom of the page. See HowtoRegisteranExperiment/Collectiontype.


Property Types

The full list of properties registered in openBIS is accessible by navigating to Admin → Types → Browse Property Types 



In the Property Browser page it is possible to:

  1. Add new properties → Entity:Add Property Type. 
  2. Edit existing properties → Entity:Edit. It is possible to change the Label and Description of the property.
  3. Delete Existing properties → Entity:Delete. Deleting a property will delete also all associated values, if the property is in use. A warning is issued: please read carefully before deleting properties!


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